Abstract Objective Copy number variation sequencing (CNV‐seq) technique was used to analyze the genetic etiology of fetuses with increased nuchal translucency (NT). Methods A total of 139 women with gestational 11‐14 weeks whose fetuses were detected with increased NT (NT ≥ 2.5 mm) in our hospital from July 2016 to December 2018 were selected. Fetal specimens were performed for karyotyping analysis and CNV sequencing. Results According to the nuchal translucency thickness, 2.5‐3.4, 3.5‐4.4, 4.5‐5.4, and more than 5.5 mm, the rates of chromosomal abnormalities were 22.8% (13/57), 30.8% (12/39), 42.1% (8/19), and 62.5% (15/24), respectively. There was significant difference among the incidences of chromosomal abnormalities in four groups (χ 2 = 37.69, P < .01) and the incidences increased with fetal NT thickness. Among 139 cases, there were 36 cases (25.9%) with abnormal chromosome karyotypes. Meanwhile, there were 45 cases (32.3%) with abnormal CNV. In the 12 cases with abnormal CNV and normal chromosome karyotypes, there were 2 cases of pathogenic CNV, 7 cases of CNV with unknown clinical significance, and 3 cases of possibly benign CNV. There was no significant difference in CNV between pregnant women in advanced maternal age and those in normal maternal age (χ 2 = 1.389, P = .239). In the fetus who showed abnormalities in NT and ultrasonography (χ 2 = 5.13, P < .05) and the fetus aborted (χ 2 = 113.19, P < .05), the abnormal rate of CNV was higher with statistically significant difference. Conclusion CNV‐seq combined karyotype analysis should be performed simultaneously in fetuses with increased NT, providing a basis for genetic counseling, which is of great significance for prenatal diagnosis.